jsbml-1.0-beta1

Version 1.0-beta1 (06-03-2014)

• New Features:
  • The main addition to JSBML 1.0 is support for the SBML Level 3 packages,
    as described below.
  • JSBML is no longer compliant with Java 1.5, and now requires Java 1.6 as
    a minimum. We believe this is reasonable given the widespread
    availability of Java virtual machines version 1.6 on diverse platforms.
  • Support for the SBML Qualitative Models package (qual) has been
    implemented, following the Version 1 Release 1 specification (17 May
    2013).
  • Support for the SBML Flux Balance Constraints package (fbc) has been
    implemented, following the Version 1 Release 1 spec. (11 February 2013).
  • Support for the SBML Hierarchical Model Composition package (comp) has
    been implemented, following the Version 1 Release 3 spec. (14 November
    2013).
  • Support for the SBML Layout package (layout) has been implemented,
    following the Version 1 Release 1 specification (13 August 2013).
  • (Experimental) support for the SBML Required Elements package (req) has
    been implemented, following the draft Version 1 Release 0.5 spec. (30 May
    2013).
  • (Experimental) support for the SBML Spatial Processes package (spatial)
    has been implemented, following the working specification Version 1
    release 0.80 (latest version is release 0.85, 13 December 2013).
  • (Experimental) support for the SBML Groups package (groups) has been
    implemented, following the draft Version 1 Release 0.4 spec. (17 May 2013).
  • (Experimental) support for the SBML Render package (render) has been
    implemented, trying to follow the SBML Level 2 specification.
  • Support for arrays, distrib and multi is not yet available but planned
    for the final JSBML 1.0 release.
  • A ParserManager class has been implemented to register SBML Level 3
    package parsers. This manager also allows JSBML to enable automatically
    the packages into the SBMLDocument so there is no longer a need to set
    the package namespace or the 'required' attribute manually.
  • Reading more than one RDF Description element in the RDF annotation
    block (the official SBML annotation scheme) is now supported. The whole
    annotation is parsed first into an XMLNode object, and then the official
    SBML annotations are extracted, if any are found.
  • A new convenience method, removeFromParent, has been added to SBase and
    TreeNodeWithChangeSupport. It offers the ability to remove any element
    from the JSBML tree from its parent.
  • An alternative class to parse mathematical formula has been implemented.
    It is named FormulaParserLL3 and it respects the same syntax as the
    libSBML L3 parser.
  • Some filter methods have been added to TreeNodeWithChangeSupport (and
    thus to SBase as well); they allow for recursive queries in the entire
    data structure.
  • A new filter, XMLNodeFilter, is available to facilitate the manipulation
    of XMLNode. It allow to do a search similar to the DOM
    Element#getElementsByTagNameNS(String, String) method on XMLNode.
  • There is now a new ProgressListener utility class that enables tracking
    the progress of computationally intensive tasks.
  • For better localization support and to separate source code from user
    messages, a new resource manager has been implemented and is being used
    in some JSBML classes already.
  • The CVTerm API has been improved with new methods that should simplify
    the code needed to manipulate CVTerm objects. The javadoc documentation
    indicates which methods could be used to replace the existing ones.
  • The libSBMLio module for reading and writing SBML using libSBML as an
    input and output module has been revised and completely re-implemented.
  • The CellDesigner plugin module has been completely re-written and has
    become significantly more efficient. This facilitates the creation of
    CellDesigner plugins for existing JSBML-based programs with very little
    overhead.
  • MAVEN support has been improved. Thanks to Aurélien Naldi for providing
    several POM.xml files for JSBML.
  • Syntax checking for SBML 'metaid' attributes have been added to the
    setMetaId method.
  • SBasePlugin now implements the TreeNodeWithChangeSupport interface.
  • Validation checks for e-mail addresses have been added to Creator.
  • A quick Hash-based search method to access elements in a model based on
    their identifier is now available. In the same way, any SBase can be
    found in the SBMLDocument based on its metaId in constant time.
  • In order to make the API more Java-like, for each getNumXXX method a
    corresponding getXXXCount method has been created.
  • The userObject in ASTNode has been replaced by a more general map of
    userObjects that is located in TreeNodeWithChangeSupport. In this way,
    any JSBML object that is part of the SBML tree can now be attached with
    user- defined objects. These will not be written to SBML later on.
  • The Unit class has the new methods removeMultiplier: it merges multiplier
    and scale. This can only be done if the logarithm to the base 10 of the
    multiplier is nearly an integer number, i.e., if the distance to the next
    integer falls below the ensured double precision.
  • The multiplyWith and divideBy methods in UnitDefinition have been
    improved to better combine units by using the merge method.
  • The Species class now ensures that its spatial size units can only be set
    if its surrounding compartment does not have zero dimensions and if its
    hasOnlySubstanceUnits attribute is false. This behavior is specified by
    the SBML documents for Level 2 Versions 1 and 2, but was not yet
    implemented.
  • When deriving its UnitDefinition, the Species class searches for a
    suitable existing unit from the model, rather than creating a new
    instance. To this end, inherited Level 3 units from the Model are now
    taken into account.
  • A new JUnit test class helps to check if simplification and merging of
    Units and UnitDefinitions works correctly.
• Bug Fixes:
  • When writing SBML to files, the streams created by JSBML were not closed
    in all cases. Fixed. Thanks to Akira Funahashi for pointing this out.
  • Appending text in an XMLToken did not have an effect if there was already
    some text. Fixed.
  • When trying to remove a modifier, reactant, or product from a reaction using
    the id of the element, where no such element was present before, a
    NullPointerException was thrown. This has been solved. Thanks to Curtis
    Madsen for detecting this bug.
  • In the Reaction class, the setReversible method accepted Boolean, instead
    of boolean. This has been changed.
  • Removed old note comment from the SubModel class.
  • JSBML did not write negative infinity into SBML files correctly. Fixed.
  • Detected and fixed a source of possible NullPointerExceptions within the
    hashCode method in ASTNode.
  • There was a bug in KineticLaw that prevented a correct iteration through
    all children. Instead of looking at the listOfLocalParameters, it
    returned the math element twice (if there was one).
  • When cloning entire models or SBMLDocuments, JSBML assigned the identical
    TreeNodeChangeListeners to the new data structure. This could lead to
    unexpected behavior because listeners were receiving change events from
    data structures to which these have not been explicitly added by a user.
  • Cloning caused problems because in some cases the recursive method that
    registers all local parameters and other entities with an id did not do a
    full recursion. Hence, some entities could not be found in the model
    later on when searching for a certain id.
  • When calling the method setSymbol in InitialAssignment with an instance
    of Variable as argument, the listeners were sometimes not correctly
    informed about changes.
  • The setParent method caused an incorrect and in many cases duplicate call
    of the nodeAdded method in TreeNodeChangeListeners. Instead of
    registering a property change (the parent link) the parent node has been
    passed to the nodeAdded method.
  • QuantityWithUnit did not fire update events when changing its value.
  • The unsetUnits method in ExplicitRule now correctly notifies the listeners.
  • The Model class lacked an unsetSubstanceUnits method. Thanks to Robert
    Byrnes for reporting this problem.
  • The Compartment class did not override the method getDerivedUnitDefinition
    from its superclass. Hence, Level 3 units could not be inherited from the
    model. Fixed.
  • Merging of Units did not correctly work in cases where the scales of two
    units could not be evenly merged: just one of both was used and the other
    was ignored. In the corrected version, both scales removed represented by
    a double-valued multiplier in the merged unit. In particular, this error
    occurred in the addition or subtraction of ASTNodes.
  • If during the simplification of UnitDefinitions a dimensionless unit was
    created by canceling terms, its scale was always set to 0 and multiplier to
    1, which could lead to errors. Additional checks now yield correct results.
  • The units of formulae containing Advogadro's number could not be derived.
    This is now fixed.
  • In some cases, containsUndeclaredUnits() in ASTNode yielded incorrect
    results. These are now fixed.
  • [Tracker item #6]: a NullPointerException was returned when using the
    method Model.findLocalParameters(String) unless at least one
    LocalParameter was registered in the model.
  • It was sometimes possible to unregister elements from a model using
    cloned elements that did not belong to the model.
  • SBMLValidator fixed according to the changes made on the sbml.org
    validator to add package information.
• Known issues:
  • If you don't have the code handling a package in your classpath,
    jsbml-1.0-beta1 will loose the package elements, they won't be kept
    in memory or went writing back the model to a file. The final release
    should be able to handle unknown packages.